[phenixbb] autogenerate restraint.eff from PDB for phenix.varref

[Nigel Moriarty]

Vincent

Can you send me your model?

Cheers

Nigel

---
Nigel W. Moriarty
Building 33R0349, Molecular Biophysics and Integrated Bioimaging
Lawrence Berkeley National Laboratory
Berkeley, CA 94720-8235
Email : NWMoriarty at LBL.gov
Web  : CCI.LBL.gov
ORCID : orcid.org/0000-0001-8857-9464


On Fri, Sep 15, 2023 at 7:46 AM vincent Chaptal <vincent.chaptal at ibcp.fr>
wrote:

> Hi Pavel,
>
> yes I do have the file which goes :
>
> geometry_restraints {
>   edits {
>     bond {
>       atom_selection_1 = chain A and resseq 1601 and name O2
>       atom_selection_2 = chain A and resseq 895 and name OG
>       distance_ideal = 3.2
>       sigma = 0.5
>     }
>     bond {
>       atom_selection_1 = chain A and resseq 1601 and name O2
>       atom_selection_2 = chain A and resseq 299 and name OG
>       distance_ideal = 2.3
>       sigma = 0.5
>     }
>
> .... many more bonds....
>
>   }
> }
>
> But it takes some time to generate a good amount of restraints, and for
> structures with several ligands it could be a long task.
> Agreed that it is not fool-proof but a general edition of these bonds and
> editing afterwards would be a good little program I believe.
>
> Best
> Vincent
>
>
> Le 15/09/2023 à 14:34, Pavel Afonine a écrit :
>
> Hi Vincent,
>
> Before launching phenix.varref, I would like to generate a ligand
> restraint file so the ligand doesn't fly away from its density.
> It would be great if the ligand_restraints.eff file could be generated
> from a PDB file already containing the ligand (for example originating from
> refinement), that we can then edit afterwards. The ligand I'm talking about
> is ATP in this case, so it doesn't need external cif file for refinement.
>
> I searched but couldn't identify such a job. It would be useful if it
> could be added to "PDB tools" or similar.
>
>
> you need to define what in Phenix is called custom bond restraints: some
> "dummy" bonds between pairs of ligand and protein atoms of your choice.
> These bonds will anchor the ligand in place. Let me know if you need help
> setting up those but I think I sent you an example some time ago.
> While generating such a file automatically is possible it may not be
> fool-proof as it will depend on the geometric quality of the model. So it's
> best to use your chemical intuition to choose those pairs of atoms that
> you'd like to link.
>
> Good luck!
> Pavel
>
>
>
>
> --
>
> Vincent Chaptal, PhD
>
> Director of GdR APPICOM
>
> Drug Resistance and Membrane Proteins Lab
>
>
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>
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>
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>
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>
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>
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>
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>
>
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